Hi,
Just to make sure that I'm clear with everything. You want to align the
anatomy using the subcortical mask or brain mask? The line below uses the
brain mask (the -cort option).
Is this for a purpose other than running FIRST? If not, the models are
still fit in the native space (it transforms the model, not the image).
The models are based on an alignment to the standard-space 1mm image.
As far as FIRST is concerned, the output image from first_flirt is only
used to check if the registration worked.
Cheers,
Brian
> Indeed - however the FIRST models (that presumably you then want to
> use after the initial flirting stage of FIRST) may be requiring that
> the standard-space version of the image is at 1x1x1mm. Brian, is that
> the case?
> Cheers.
>
>
> On 29 Jan 2009, at 06:44, wolf zinke wrote:
>
>> Hi Mark,
>>
>> You might modify the script (/usr/local/fsl/bin/first_flirt) to
>> achieve this. In line 130 there is a final flirt call to apply the
>> transformation:
>> ${FSLDIR}/bin/flirt -in ${A} -out ${B} -ref ${FSLDIR}/data/standard/$
>> {refim} -applyxfm -init ${B}_cort.mat
>>
>> If you change it to
>> ${FSLDIR}/bin/flirt -in ${A} -out ${B} -ref ${A} -applyxfm -init $
>> {B}_cort.mat
>>
>> I guess this could do the trick. Another option might be to change
>> the reference image (line 90: refim=MNI152_T1_1mm) and use one that
>> you created for your purpose. However, you still might notice a
>> degradation of the image quality that is due to the interpolation
>> (add '-interp sinc' to the last flirt call to whether it improves).
>>
>> good luck,
>> wolf
>>
>> Mark Schira wrote:
>>> Hi
>>> I ma trying to use the first_flirt script to rotate anatomy scans
>>> into a
>>> standard space.
>>> first_flirt seems to do the job, however it also resizes the images
>>> into a
>>> standard resolution of 1x1x1 mm, thereby significantly reducing the
>>> quality
>>> of the data, which is in 0.75mm. (The reduction of quality is
>>> rather dramatic!).
>>>
>>> So in other words I want to do exactly what first_flirt does, but
>>> without
>>> resizing to 1mm, but instead simply applying a rotation and
>>> translation.
>>> I looked hard but I couldn't identify an option for this, nor could
>>> I see
>>> where in the first_flirt script i would have to make the changes...
>>> Cheers
>>> M.
>>>
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
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